Contributing¶

Please join our effort. We welcome new contributors to assist with the development of BioKotlin.

Where to start¶

• Discussions
• ask questions and propose ideas.
• Issues - report bugs and pick up work.
• Trello board - what the team is working on.
• New to pull requests? Atlassian has a good walkthrough.

Code examples are especially welcome. If you have a notebook that shows off something BioKotlin does well, open a discussion or a pull request - the tutorials on this site are generated directly from notebooks in the repository.

Working on the library¶

git clone https://github.com/maize-genetics/BioKotlin.git
cd BioKotlin
./gradlew build

Tests run with ./gradlew test and use Kotest and JUnit 5. Opening a pull request against master runs the suite in CI.

Working on this website¶

The site lives in the same repository and is built with Zensical. Pages are Markdown under docs/, and the tutorials are generated from the notebooks under notebooks/.

python -m venv .venv && source .venv/bin/activate
pip install -r website/requirements.txt

python website/convert_notebooks.py --no-execute   # generate tutorial pages
zensical serve                                     # preview at localhost:8000

website/README.md has the full details, including how to re-execute the notebooks and how the runnable code snippets are wired up.